Studies performed using magnetically labeled lymph node derived cells in the marmoset EAE model have shown the ability to detect labeled cells in the brain and spinal cord on a clinical MRI scanner. These results will serve as the basis for moving forward to magnetically label cells harvested during apheresis and re-infuse autologous cells into patients with MS to monitor the migration of labeled stem cells or peripheral blood mononuclear cells into the central nervous system by MRI. In the marmoset EAE model immunohistochemical techniques were used to identify and describe cortical lesions in marmosets with experimental autoimmune encephalomyelitis (EAE). Using antibodies to proteolipid protein (PLP) cortical lesions in were identified in animals. These lesions were subdivided into leucocortical, intracortical and subpial lesions. The density of inflammatory cells within lesions using a double labeling protocol which employed anti-PLP in addition to antibodies against markers of B-lymphocytes (CD20), T-lymphocytes (CD3), macrophages (MAC387) and MHC-II expressing cells (CR3/43). This analysis revealed that the large subpial lesions accounted for the majority of demyelinated cortex despite possessing the lowest density of inflammatory cells. This study has shown that lesions in this model share many of the major features of cortical lesions in MS both in terms of morphology and inflammatory cell content.